Reading DNA Sequencing Charts (Chromatograms)
Read a DNA sequence base by base from a Sanger chromatogram, and spot a heterozygous site where two colored peaks overlap at one position.
A DNA sequencing machine does not print letters, it prints a chromatogram: a row of colored peaks, one color for each base. If you cannot read that chart, you cannot check the machine's work, and the machine is not always right. Reading a chromatogram is how you confirm a base call, catch a messy peak, and above all recognize a heterozygous site, where two peaks stack up at one position because the person carries two different alleles. Clinical geneticists and genetic counselors read these traces to confirm a disease-causing variant before telling a family. Forensic DNA analysts read them to call a profile that will hold up in court. Microbiologists read them to identify a pathogen from its sequence, and researchers in labs like the ones at John Hay's partner universities read them every day to verify that a gene was cloned correctly. The base calls a computer prints are a starting point, not the final answer. The person who can read the raw peaks is the person who is trusted with the result.
- NGSS · SEP-4Analyzing and Interpreting Data: read a graphical readout (a chromatogram) and translate the pattern of peaks into the DNA sequence it represents.
- Common Core · HSS-ID.A.1Represent and interpret data displayed in a plot; here, read position and peak height to extract the underlying values (the base at each position).
- Ohio · Ohio HS Bio.DHAnalyze and interpret biological data, including reading instrument output such as a DNA sequencing trace, to draw supported conclusions.
- AP · AP Bio SP 4 (Data)Analyze and evaluate data; interpret a graphical dataset (the electropherogram) and identify what a single overlapping peak means for genotype.
- NGSS · SEP-5Using Mathematics and Computational Thinking: use position order and relative peak height to reason quantitatively about which base was read and how confident the call is.
- Know the four DNA bases (A, C, G, T): You are reading a chart whose whole job is to report which of the four bases is at each spot, so the bases must be second nature.
- Read position and height on a simple plot: A chromatogram is a plot: left-to-right is position, up is signal strength, so basic graph reading transfers directly.
- Understand alleles and genotype (two copies of a gene): The double-peak idea only makes sense once a student knows a person carries two alleles that can differ.
Prerequisites are inferred: pending teacher review.
Re-learn the skill with worked practice and clear examples.
Read a real trace one position at a time: go left to right, and at each position name the base from the peak's color. When a position shows two overlapping half-height peaks instead of one, that position is a heterozygous site and you record both bases.
Read the four single peaks in the chart, left to right, using A = green, C = blue, G = black, T = red. What is the sequence?
Reviewed- A.A C G T
- B.G C A T
- C.A G C T
- D.T G C A
Show the worked solution ▾
Answer: A. A C G T
- Step 1: Position 1: Green peak, and green is A.
- Step 2: Position 2: Blue peak, and blue is C.
- Step 3: Position 3: Black peak, and black is G.
- Step 4: Position 4: Red peak, and red is T. So the sequence is A C G T.
Why it's right: Reading left to right, the colors green, blue, black, red map to A, C, G, T, giving A C G T.
- B: This swaps the first (green = A) and third (black = G) peaks.
- C: This swaps the middle two peaks (blue = C and black = G).
- D: This reads the peaks right to left, reversing the sequence.
Aligned to NGSS SEP-4: translate peak colors into a sequence · reading level ~grade 9
In a chromatogram, one position shows two peaks stacked on top of each other, each at about half the normal height, while every other position has one full peak. What does that one position most likely mean?
Reviewed- A.The machine ran out of ink at that spot
- B.That position is a heterozygous site with two different bases
- C.The sequence should be read backward from there
- D.Nothing, half-height peaks are always ignored
Show the worked solution ▾
Answer: B. That position is a heterozygous site with two different bases
- Step 1: Name the pattern: Two overlapping peaks at one position, each about half height, is the classic double-peak pattern.
- Step 2: Interpret it: It means two different bases were read there, one from each allele, so the person is heterozygous at that position.
Why it's right: Two half-height peaks stacked at a single position is the signature of a heterozygous site, where the two alleles carry different bases.
- A: Sequencers do not use ink, and this is a real signal, not a printing gap.
- C: A double peak marks a genotype, it does not change the read direction.
- D: A clear double peak is meaningful and should be recorded, not ignored.
Aligned to Ohio HS Bio.DH: interpret a data feature · reading level ~grade 9
Use the trace to genotype the marked position. Every other position is a single clean peak, but the marked position shows a green peak and a red peak overlapping at half height each (A = green, C = blue, G = black, T = red). What is the genotype at that position?
Reviewed- A.Homozygous G
- B.Homozygous C
- C.Heterozygous A / T
- D.Heterozygous C / G
Show the worked solution ▾
Answer: C. Heterozygous A / T
- Step 1: Look at the marked position: It has two peaks, not one, so it is a heterozygous site.
- Step 2: Read both colors: The two overlapping peaks are green and red. Green is A and red is T.
- Step 3: Write the genotype: Two different bases at one site means the genotype is A / T.
Why it's right: The marked position has two half-height peaks, green and red, which are A and T, so the genotype there is heterozygous A / T.
- A: The marked position has two peaks, so it is not homozygous, and neither peak is black (G).
- B: The marked position has two peaks, so it is not homozygous, and neither peak is blue (C).
- D: The two overlapping colors are green and red (A and T), not blue and black (C and G).
Aligned to NGSS SEP-4: call a genotype from a double peak · reading level ~grade 9
- A lab technician reads a 20-base trace by hand to confirm the software's base calls before signing off on the result.
- A genetics student marks every double peak in a patient trace so the class can list which positions are heterozygous.
- A researcher checks that a cloned gene's trace is one clean peak per position, proving no unwanted mutation slipped in.
Fill these in as you work through the lesson.
- Chromatogram (the colored-peak chart from a sequencer):
- Base call (the base read from a peak's color):
- Heterozygous site (two overlapping peaks at one position):
- Peak height (how strong and trustworthy the signal is):
Read the chart from to , name each base from the peak's , and when one position shows overlapping half-height peaks, record it as a site with two different bases.
- Using A = green, C = blue, G = black, T = red, what base does a blue peak stand for?
- How is a heterozygous position different from a homozygous position on the trace?
- Why might a short, noisy peak need to be resequenced instead of trusted?
A trace shows, left to right, a green peak, a black peak, then one position with a blue and a red peak overlapping at half height each. The first two bases are ____ and ____, and the third position is a heterozygous ____ / ____ site.
The vocabulary of this topic, shown in the way you will meet it.